The primary modeling tool used on the cluster is the CHARMM (Chemistry at HARvard Molecular Mechanics) software package. Dr. Bernard Brooks, the head of the LCB, is one of the primary developers of CHARMM. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the package.

Another piece of commercial software that performs quantum calculations is Q-Chem. Q-Chem uses efficient techniques to parallelize methods such as Hartree-Fock and DFT single-point energies, geometry optimizations, and frequency calculations. Q-Chem combines these advanced techniques into a single package for use in ab initio computations. Q-Chem is also capable of performing QM/MM calculations via a CHARMM QM/MM interface.

For ab initio quantum mechanical calculations we have available GAMESS-US and GAMESS-UK. Both software packages provide means of performing QM/MM calculations via a CHARMM QM/MM interface.

VMD is a multiplatform molecular visualization program. It supports many different coordinate and structure file formats, including those used by CHARMM, PQR, and AMBER. It also is able to read GAMESS log files. We use it to create beautifully rendered images of the molecular systems which we study (some of which can be found on this Web site).

Compilers and Parallel Execution Tools

Most of our compiling is done with the open-source GNU Compiler Collection. The version of MPICH that we currently use is compiled with version 3.3.3 of gcc.

The Portland Group compiler suiteis a set of high-end compilers for Fortran (77 and 90), C, and C++ that are designed to work in high performance computing environments. We compile some of our parallel code with these compilers.

MPICH is a portable implementation of the MPI parallel computing standard. The software was developed at Argonne National Laboratory. We currently use the 1.2.5 series, but MPICH-2, which supports both the MPI-1 and MPI-2 standards, is now available. The parallel CHARMM jobs we run on LoBoS use MPICH to handle their MPI functionality.

Open MPI: The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the experise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

LA-MPI is another implementation of the MPI standard, developed at Los Alamos National Laboratory. It is no longer in active development, but existing versions continue to be maintained. Development efforts are focusing on releasing Open MPI.

We use Myricom products for low latency network communication, we also use the GM drivers to power our Myrinet communications. We're currently using a custom-built version of GM

Administrative and Monitoring Software

The LoBoS job scheduler is the TORQUE Resource Manager disributed by Cluster Resources, Inc.. We currently use version 1.1.0p6 with a couple of small patches by Tim Miller and others. TORQUE is an improvement over OpenPBS and in tests it has been able to scale to managing over one thousand jobs simulataneously.

We've found Nagios useful for general cluster monitoring and supervising important systems such as our RAID arrays. Nagios can automatically notify an administrator by e-mail when it detects a problem.

For performance monitoring, we also have Ganglia configured. Ganglia is useful because it requires little configuration and scales well.

Miscellaneous

We use GNUPlot for many of our graphing needs. This software makes it easy to create good looking graphs of data on the Unix command line.